IAO-and-BFO-Oct-2013.. - Buffalo Ontology Site

Report
Social Event, Monday, November 18, 6pm
The Information Artifact Ontology:
Roots in BFO
Barry Smith
October 14, 2013
Continuant
Independent
Continuant
Occurrent
Dependent
Continuant
Process
Quality
Realizable
Dependent
Continuant
Disposition
Role
3
Types and Instances
Geographic
Coordinate
s Set
designate
s
Spatial
Region
instance_
of
has
location
Distance
Measurement
Result
Geopolitical
Entity
has
location
designates
instance_of
Village
Well
Latrin
e
instance_of
is_a
Village
Name
instance_
of
instance_o
f
instance_
of
’16 meters’
‘VT 334
569’
measurement_of
locate
d near
‘Khanabad
Village’
located
in
4
Continuant
Independent
Continuant
Quality
Disposition
Specifically
Dependent
Continuant
Realizable
Dependent
Continuant
Generically
Dependent
Continuant
Gene
Sequence
Information
Artifact
Role
5
Specifically Dependent Continuants
Specifically
Dependent
Continuant
has unique bearer; if this
bearer ceases to exist, then
the quality or RDC ceases to
exist
the color of my skin
the function of my heart
John’s smile
Quality, Pattern
Realizable
Dependent
Continuant
(RDC)
6
Generically Dependent Continuants
Generically
Dependent
Continuant
if one bearer ceases to exist, then
the entity can survive, because
there are other bearers
(copyability)
the pdf file on my laptop
Information
Object
Sequence
the DNA (sequence) in this
chromosome
7
Information artifacts
pdf file
email
poem
symphony
algorithm
symbol
- can migrate from one information bearer to another
8
Continuant
Independent
Continuant
Material
Entity
Specifically
Dependent
Continuant
Quality
Generically
Dependent
Continuant
Gene
Sequence
Information
Artifact
Information
Bearing
Entity
9
Continuant
Independent
Continuant
Material
Entity
Information
Bearing
Entity
Specifically
Dependent
Continuant
Quality
depends_on
Information
Quality
Entity
Generically
Dependent
Continuant
Information
Artifact
concretized_by
10
http://bioportal.bioontology.org/ontologies/IAO
11
IAO: information content entity
=def. an entity that is generically
dependent on some artifact and stands in
the relation of aboutness to some entity
Problems
Is a work of fiction about something?
Is a fake cover story for a fake terrorist about
something?
Is an erroneous entry in a database about
something?
12
Generically dependent continuants such as
plans, laws …
are concretized in specifically dependent continuants
(the plan in your head, the protocol being realized by your
research team, the law being implemented by this
government agency)
13
War and Peace is an instance
Specifically
Dependent
Continuant
Independent
Continuant
instance_of
This bound
copy of
War and Peace
instance_of
War and Peace
depends_on
quality
Generically
Dependent
Continuant
instance_of
The novel
War and Peace
14
15
Instances vs Copies
The novel War and Peace has many bound
copies
The quality spherical has many instances
But having copies and having instances are two
different things
Information entities exist in a way which makes
them dependent on provenance, and on
processors, in a way in which types are not
16
What is a work of literature?
Is War and Peace a type or an instance?
•
If War and Peace were a type, and the copies of War and
Peace in my library and in your library were instances,
then
there would be many War(s) and Peaces.
Hence War and Peace is an instance.
17
There are not two Declarations of
Independence
There can be two copies of the US Declaration
of Independence
There cannot be two US Declarations of
Independence
There cannot be subtypes of the US
Declaration of Independence
Hence the US Declaration of Independent is an
instance and not a type.
18
Rule for types
Their names are pluralizable
There can be three people
There cannot be three Michelle Obamas.
Information Content Entities are GDCs = entities which can
exist in many copies
19
Generically dependent continuants are distinct
from types
they have a different kind of
provenance
◦ Aspirin as product of Bayer GmbH
◦ aspirin as molecular structure
◦ This Financial Report is submitted to the
SEC
20
Generically dependent continuants
are concretized in specifically dependent
continuants
Beethoven’s 9th Symphony is concretized in the
pattern of ink marks which make up this score in
my hand – this is an information quality entity: a
BFO:quality of the material (information bearing
entity) that is the score
23
Generically dependent continuants (GDCs)
can be concretized in multiple different
media (paper, silicon, neuron …)
24
Type or instance
Continuant
Independent
Continuant
human being,
protocol
document
Dependent
Continuant
pattern of
ink marks
Occurrent
(Process)
Applying
the protocol
Side-Effect …
... .. ..... .... .....
26
Continuant
Independent
Continuant
Occurrent
Dependent
Continuant
Information
Content
Entity
.... .....
Action
creating a datum
.......
27
Generically dependent continuants
do not require specific media (paper,
silicon, neuron …)
28
Generically Dependent Continuants
Generically
Dependent
Continuant
Information
Content Entity
.pdf file
Gene
Sequence
.doc file
instances
29
Generically dependent continuants
are concretized in specifically
dependent continuants
Beethoven’s 9th Symphony is
concretized in the pattern of ink
marks which make up this score in
my hand
30
Steps towards an email ontology
•
•
•
•
message has_part header section and body section
header section has_part a collection of header fields
header field contains a header name and a header
body
header body may have additional structure based on
the header in question
• body may have nested structure and attachments based on
MIME
• the body may contain a text version, an HTML version, or
both
• the body may contain attachments (files such as images,
documents, other emails, etc
•
header fields may use MIME to include header
information in other languages/charsets
Steps towards an email ontology
email may have_status draft, sent
email may addressee may be in to: field, cc: field,
bcc: field
email may be forwarded
email may be read, unread
email may have priority
…
32
E-mail Header
33
Email Address Field
A field is an information structure entity
(comparable to cell, margin, space between words, period, comma, etc.)
This means it is not about anything.
Nearly all information content entities have fields as parts
Address field is an information content entity which has a field as part
But address field is about (in some very attenuated sense) the type: address
Similarly the field in a spreadsheet where you fill in the measurement unit used is an ICE, because it is (in
this same attenuated sense) the type: measurement unit.
When you fill in the actual address then the resultant field is an ICE which is about that actual address
BS
34
Email address
Good. Well sort of. What is the type "address" here?
Below it is another information content entity.
Sometimes the address means the "mailbox", i.e.
an entity on the other side of a future
communication, rather than an entity on the form.
Sometimes it is about the target/owner of the email
address, for instance when it is used as a user
name in an online authentication form.
35
Sometimes, even the idea that the email address is
of an addressee fails. For example email can be
used as a request for a service. An example is
when we send mail to "[email protected]",
where it is known that software will intercept such
emails, extract the string after "From:", and remove
from the mailing list any email address with that
form. In that case the email address seems more to
be about some kind of role, where the realization of
36
Purpose of an Information Artifact
Descriptive purpose
=def. the purpose of describing some portion of reality
Examples: scientific paper, newspaper article, diary, experimenter
log notebook
Prescriptive purpose
=def. the purpose of prescribing or permitting or allowing some
activity
Examples: a legal code, a license
37
Purpose of an Information Artifact
Directive purpose
=def. the purpose of specifying a plan or method for achieving
something
Examples: instruction, manual, recipe, protocol
Designative purpose
=def. the purpose of uniquely designating some entity or the
members of some class of entities
Examples: a registry of members of an organization, a phone book,
a database linking proper names of persons with their social
security numbers.
38
40
Information Content Entity (science)
protocol
database
theory
ontology
gene list
publication
result
...
41
Information Content Entity
(labeling)
serial number
batch number
grant number
person number
name
address
email address
URL
...
42
43
44
Information Content Entity (Finance)
•
•
•
Financial Report
Financial Report in XBRL for submission to GAAP
Business Report
45

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